BACKGROUND Gallbladder neuroendocrine carcinoma(NEC)represents a subtype of gallbladder malignancies characterized by a low incidence,aggressive nature,and poor prognosis.Despite its clinical severity,the genetic alte...BACKGROUND Gallbladder neuroendocrine carcinoma(NEC)represents a subtype of gallbladder malignancies characterized by a low incidence,aggressive nature,and poor prognosis.Despite its clinical severity,the genetic alterations,mechanisms,and signaling pathways underlying gallbladder NEC remain unclear.CASE SUMMARY This case study presents a rare instance of primary gallbladder NEC in a 73-year-old female patient,who underwent a radical cholecystectomy with hepatic hilar lymphadenectomy and resection of liver segments IV-B and V.Targeted gene sequencing and bioinformatics analysis tools,including STRING,GeneMANIA,Metascape,TRRUST,Sangerbox,cBioPortal and GSCA,were used to analyze the biological functions and features of mutated genes in gallbladder NEC.Twelve mutations(APC,ARID2,IFNA6,KEAP1,RB1,SMAD4,TP53,BTK,GATA1,GNAS,and PRDM3)were identified,and the tumor mutation burden was determined to be 9.52 muts/Mb via targeted gene sequencing.A protein-protein interaction network showed significant interactions among the twelve mutated genes.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were used to assess mutation functions and pathways.The results revealed 40 tumor-related pathways.A key regulatory factor for gallbladder NEC-related genes was identified,and its biological functions and features were compared with those of gallbladder carcinoma.CONCLUSION Gallbladder NEC requires standardized treatment.Comparisons with other gallbladder carcinomas revealed clinical phenotypes,molecular alterations,functional characteristics,and enriched pathways.展开更多
Bioinformatics,an interdisciplinary field that integrates computer science,biology,information technology,and statistics,plays a pivotal role in analyzing and interpreting biological data.It has become an indispensabl...Bioinformatics,an interdisciplinary field that integrates computer science,biology,information technology,and statistics,plays a pivotal role in analyzing and interpreting biological data.It has become an indispensable tool in the design and discovery of novel drugs by facilitating the analysis of biological datasets and aiding in the identification of potential therapeutic targets.With the rise of antibiotic resistance among bacterial species,the demand for new drug development has intensified.However,the process of drug discovery remains labor-intensive,costly,and time-consuming.The identification of new drugs involves multiple critical stages,including target identification,structural analysis of the target protein,selection of potential drug candidates,safety and efficacy assessments,drug optimization,and ultimately,validation.Bioinformatics contributes significantly to each of these phases.For instance,through the analysis of protein sequences and genetic data,researchers can pinpoint potential drug targets.Once a target protein is identified,bioinformatics tools enable detailed structural analysis of the protein.Upon locating the potential ligand-binding site,large compound databases can be screened to discover viable drug candidates.Simulations further aid in examining the interaction between the target protein and biomolecules,providing valuable insights into the drug’s safety and efficacy.Moreover,bioinformatics-driven drug optimization helps improve both safety and effectiveness.Recent advances,such as pharmacophore modeling and molecular docking techniques,have accelerated the screening process,narrowing thousands of candidate molecules down to a select few with promising therapeutic potential.In this study,bioinformatics was leveraged within the framework of network pharmacology to design and discover new drugs.展开更多
BACKGROUND Myocardial ischemia/reperfusion(I/R)injury,which is associated with high morbidity and mortality,is a main cause of unexpected myocardial injury after acute myocardial infarction.However,the underlying mech...BACKGROUND Myocardial ischemia/reperfusion(I/R)injury,which is associated with high morbidity and mortality,is a main cause of unexpected myocardial injury after acute myocardial infarction.However,the underlying mechanism remains unclear.Circular RNAs(circRNAs),which are formed from protein-coding genes,can sequester microRNAs or proteins,modulate transcription and interfere with splicing.Authoritative studies suggest that circRNAs may play an important role in myocardial I/R injury.AIM To explore the role and mechanism of circRNAs in myocardial I/R injury.METHODS We constructed a myocardial I/R injury model using ligation of the left anterior descending coronary artery,and evaluated the success of the validated model using triphenyltetrazolium chloride and hematoxylin-eosin staining.Then,left ventricular samples from different groups were selected for mRNA-sequence,and differential gene screening was performed on the obtained results.The differentially obtained mRNAs were divided into up-regulated and down-regulated according to their expression levels,and Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)functional enrichment analysis were performed,respectively.Then,the obtained circRNA and microRNA(miRNA)were paired for analysis,and the binding sites of miRNA and mRNA were virtual screened.Finally,the obtained circRNA,miRNA and mRNA were constructed by ceRNA mutual most useful network.RESULTS We used an RNA sequencing array to investigate the expression signatures of circRNAs in myocardial I/R injury using three samples from the I/R group and three samples from the sham group.A total of 142 upregulated and 121 downregulated circRNAs were found to be differentially expressed(fold change≥2,P<0.05).GO and KEGG functional analyses of these circRNAs were performed.GO analysis revealed that these circRNAs were involved mainly in cellular and intracellular processes.KEGG analysis demonstrated that 6 of the top 20 pathways were correlated with cell apoptosis.Furthermore,a circRNA-miRNA coexpression network and ceRNA network based on these genes were constructed,revealing that mmu-circ-0001452,mmu-circ-0001637,and mmu-circ-0000870 might be key regulators of myocardial I/R injury.CONCLUSION This research provides new insights into the mechanism of myocardial I/R,which mmu-circ-0001452,mmu-circ-0001637,and mmu-circ-0000870 are expected to be new therapeutic targets for myocardial I/R injury.展开更多
As a high-value eudicot family,many famous horticultural crop genomes have been deciphered in Oleaceae.However,there are currently no bioinformatics platforms focused on empowering genome research in Oleaceae.Herein,w...As a high-value eudicot family,many famous horticultural crop genomes have been deciphered in Oleaceae.However,there are currently no bioinformatics platforms focused on empowering genome research in Oleaceae.Herein,we developed the first comprehensive Oleaceae Genome Research Platform(OGRP,https://oleaceae.cgrpoee.top/).In OGRP,70 genomes of 10 Oleaceae species and 46 eudicots and 366 transcriptomes involving 18 Oleaceae plant tissues can be obtained.We built 34 window-operated bioinformatics tools,collected 38 professional practical software programs,and proposed 3 new pipelines,namely ancient polyploidization identification,ancestral karyotype reconstruction,and gene family evolution.Employing these pipelines to reanalyze the Oleaceae genomes,we clarified the polyploidization,reconstructed the ancestral karyotypes,and explored the effects of paleogenome evolution on genes with specific biological regulatory roles.Significantly,we generated a series of comparative genomic resources focusing on the Oleaceae,comprising 108 genomic synteny dot plots,1952225 collinear gene pairs,multiple genome alignments,and imprints of paleochromosome rearrangements.Moreover,in Oleaceae genomes,researchers can efficiently search for 1785987 functional annotations,22584 orthogroups,29582 important trait genes from 74 gene families,12664 transcription factor-related genes,9178872 transposable elements,and all involved regulatory pathways.In addition,we provided downloads and usage instructions for the tools,a species encyclopedia,ecological resources,relevant literatures,and external database links.In short,ORGP integrates rich data resources and powerful analytical tools with the characteristic of continuous updating,which can efficiently empower genome research and agricultural breeding in Oleaceae and other plants.展开更多
This study aimed to investigate the role of autophagy-related genes in osteoarthritis(OA)and evaluate the therapeutic potential of Eucommin A,a key lignan component derived from Eucommia ulmoides.Gene expression profi...This study aimed to investigate the role of autophagy-related genes in osteoarthritis(OA)and evaluate the therapeutic potential of Eucommin A,a key lignan component derived from Eucommia ulmoides.Gene expression profiles from OA patients and healthy controls were retrieved from the Gene Expression Omnibus(GEO)database.Differentially expressed genes(DEGs)were identified and intersected with autophagy-related genes from the Human Autophagy Database to pinpoint OA-specific autophagy candidates.Functional enrichment analyses via GO and KEGG highlighted involvement in nutrient response,apoptosis,and PI3K-Akt/FoxO signaling pathways.Core genes were prioritized using machine learning algorithms combined with protein-protein interaction(PPI)network analysis,followed by diagnostic validation in an independent cohort.Molecular docking and 100-ns molecular dynamics simulations were conducted to assess the binding stability between Eucommin A and the core targets.Interaction mechanisms were characterized using root mean square deviation(RMSD),root mean square fluctuation(RMSF),radius of gyration(Rg),and MM/GBSA binding free energy calculations.Among 2436 DEGs,56 were autophagy-related and significantly enriched in key biological processes.Machine learning identified EGFR,MAPK3,and MAPK8 as hub genes,with EGFR and MAPK8 exhibiting significant diagnostic value(AUC>0.5).Eucommin A demonstrated strong binding affinity to EGFR and MAPK8 via hydrogen bonding and hydrophobic interactions.Molecular dynamics simulations confirmed stable ligand-target complexes and favorable binding free energy profiles.These findings suggested EGFR and MAPK8 as diagnostic biomarkers for OA-related autophagy.Moreover,Eucommin A exerted multi-target therapeutic effects by stabilizing these autophagy-related proteins,proposing a novel strategy for OA treatment through modulation of autophagy.展开更多
Objective:Employing bioinformatics methodologies to identify core genes intricately associated with the pathogenesis and progression of gastric cancer,and to evaluate their clinical significance.Method:Gene expression...Objective:Employing bioinformatics methodologies to identify core genes intricately associated with the pathogenesis and progression of gastric cancer,and to evaluate their clinical significance.Method:Gene expression datasets GSE19826 and GSE13911 were acquired from the Gene Expression Omnibus(GEO).Differential gene expression analysis was conducted using GEO2R.Common differentially expressed genes(DEGs)were discerned via Venn diagram analysis on a bioinformatics platform.Functional enrichment analyses,including Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG),were performed on these overlapping DEGs.A protein-protein interaction(PPI)network was constructed with the STRING database,and central hub genes were identified using Cytoscape software.The expression profiles,prognostic value,and immune infiltration correlations of these key genes were further examined utilizing the GEPIA,Kaplan-Meier plotter,Human Protein Atlas(HPA),and TIMER databases.Results:Analysis revealed 120 commonly differentially expressed genes.These genes were significantly enriched in biological pathways concerning muscle cell cytoskeleton regulation,nutrient absorption,and extracellular matrix receptor interactions.PPI network analysis highlighted 10 core genes,including COL1A1,COL1A2,BGN,THBS2,COL5A2,and TIMP1.These genes exhibited marked upregulation in GC tissues.Statistical evaluation confirmed a significant link between their elevated expression and unfavorable patient outcomes(P<0.01).Furthermore,immune infiltration assessment indicated a positive correlation between the expression of these genes and macrophage infiltration within the tumor microenvironment,implying their involvement in modulating the immune response in GC,which could affect tumor behavior and clinical progression.Conclusion:The six genes identified may function as diagnostic biomarkers and represent promising therapeutic targets for gastric cancer.展开更多
Objective:To investigate the potential targets and mechanisms of Draconis Sanguis(DS),a valuable traditional Chinese medicine derived from the resin of the palm tree Daemonorops draco Bl(D.Sanguis,Xue Jie),in the trea...Objective:To investigate the potential targets and mechanisms of Draconis Sanguis(DS),a valuable traditional Chinese medicine derived from the resin of the palm tree Daemonorops draco Bl(D.Sanguis,Xue Jie),in the treatment of myocardial infarction(MI).Methods:We explored the potential mechanisms of DS in the treatment of MI using network pharmacology,bioinformatic techniques,and transcriptomic analysis,followed by validation through in vivo and in vitro experiments.Results:Network pharmacology and bioinformatic analyses identified five genes(Fpr1,Glul,Mme,Mmp9,and Pla2g7)as potential targets for MI treatment.Moreover,DS significantly ameliorated cardiac function,inflammatory responses,and MI-induced myocardial fibrosis in vivo.Transcriptomic and bioinformatic analyses identified Pla2g7 as the most critical target in the DS treatment of MI.Molecular docking revealed that the key active ingredient in DS has a strong affinity for this gene.Furthermore,DS reduced the expression of Pla2g7(P=.0009),NLRP3(P=.003),interleukin-18(P<.001),and interleukin-1b(P=.004)mRNAs in vivo.Conclusions:The results indicate that DS can downregulate the expression of Pla2g7 and reduce the inflammatory response.This demonstrates the potential therapeutic target of DS and the mechanism underlying its cardioprotective effects.展开更多
BACKGROUND Esophageal cancer(ESCA)poses a significant challenge in oncology because of the limited treatment options and poor prognosis.Therefore,enhancing the therapeutic effects of radiotherapy for ESCA and identify...BACKGROUND Esophageal cancer(ESCA)poses a significant challenge in oncology because of the limited treatment options and poor prognosis.Therefore,enhancing the therapeutic effects of radiotherapy for ESCA and identifying relevant therapeutic targets are crucial for improving both the survival rate and quality of life of patients.AIM To define the role of the transcription factor Snail family transcriptional repressor 1(SNAI1)in ESCA,particularly its regulation of radiosensitivity.METHODS A comprehensive analysis of TCGA data assessed SNAI1 expression in ESCA.Survival curves correlated SNAI1 levels with radiotherapy outcomes.Colony formation assays,flow cytometry,and a xenograft model were used to evaluate tumor radiosensitivity and apoptosis.Western blot validated protein expression,while Chromatin im-munoprecipitation assays examined SNAI1's role in regulating epithelial-mesenchymal transition(EMT).RESULTS SNAI1 expression in ESCA cell lines and clinical specimens emphasizes its central role in this disease.Elevated SNAI1 expression is correlated with unfavorable outcomes in radiotherapy.Downregulation of SNAI1 enhances the sensitivity of ESCA cells to ionizing radiation(IR),resulting in remarkable tumor regression upon IR treatment in vivo.This study underscores the direct involvement of SNAI1 in the regulation of EMT,particularly under IR-induced conditions.Furthermore,inhibiting deacetylation effectively suppresses EMT,suggesting a potential avenue to enhance the response to radiotherapy in ESCA.CONCLUSION This study highlights SNAI1's role in ESCA radiosensitivity,offering prognostic insights and therapeutic strategies to enhance radiotherapy by targeting SNAI1 and modulating EMT processes.展开更多
[Objectives]To develop a pair of specific primers for the PCR amplification of the full-length relA gene from Vibrio alginolyticus strain HY9901,as well as to conduct bioinformatics analysis.[Methods]The relA gene was...[Objectives]To develop a pair of specific primers for the PCR amplification of the full-length relA gene from Vibrio alginolyticus strain HY9901,as well as to conduct bioinformatics analysis.[Methods]The relA gene was amplified through PCR,and the resulting gene sequence was subsequently analyzed using bioinformatics tools,including amino acid sequence prediction,functional site analysis,subcellular localization prediction,and homology comparison.[Results]The relA gene had a total length of 2220 bp and encoded 739 amino acid residues.The molecular weight was approximately 84.1261 kDa,and its isoelectric point was 5.95.The protein lacked a signal peptide and transmembrane regions,while exhibiting multiple phosphorylation sites.Predictions regarding its subcellular localization suggested that it was predominantly situated in the cytoplasm.The amino acid sequence demonstrated a homology of 97%to 99%with other species within the genus Vibrio,and it clustered within the same subfamily as V.antiquarius and V.diabolicus.In the prediction of secondary structure,the proportions ofα-helix,extended strand,random coil,andβ-sheet were 54.13%,12.04%,28.15%and 5.68%,respectively.The similarity between the tertiary structure model and template 5kpw.1.w was 66%.[Conclusions]In this study,the relA gene of V.alginolyticus strain HY9901 has been successfully amplified and analyzed.The structural characteristics and potential functions of the encoded protein have been elucidated,thereby providing foundational data for understanding the role of this gene in V.alginolyticus.展开更多
Kinesins are a superfamily of proteins widely present in eukaryotes,playing crucial roles in plant cell wall assembly,cell elongation regulation,gravity sensing,and fertility control.In this study,bioinformatics analy...Kinesins are a superfamily of proteins widely present in eukaryotes,playing crucial roles in plant cell wall assembly,cell elongation regulation,gravity sensing,and fertility control.In this study,bioinformatics analysis of the OsKMP2 gene(LOC_Os02g28850)was performed using online tools such as ExPASy-ProtParam,ProtScale,CD-search,and DNAMAN software.Additionally,qRT-PCR was employed to analyze the tissue expression pattern of OsKMP2.The results showed that the molecular weight of the OsKMP2 is 118.39728 kDa,and it is a hydrophilic and unstable acidic protein.Secondary structure prediction revealed that it primarily consists ofα-helices(69.45%),random coils(25.19%),and extended strands(5.36%).The gene was expressed in various rice tissues,with the highest expression level observed in leaves.These results indicate that the OsKMP2 gene exhibits high evolutionary conservation and functional diversity in rice.展开更多
[Objectives] To analyze the function of cobQ gene from Vibrio alginolyticus strain HY9901,and to provide a reference for exploring the possible mechanism of cobQ gene from V.alginolyticus.[Methods] A pair of primers w...[Objectives] To analyze the function of cobQ gene from Vibrio alginolyticus strain HY9901,and to provide a reference for exploring the possible mechanism of cobQ gene from V.alginolyticus.[Methods] A pair of primers were designed based on the sequence of the V.alginolyticus cobQ gene and used to amplify the full-length gene by PCR.[Results] The PCR amplification results indicated that the cobQ gene has a full length of 780 bp,encoding 259 amino acid residues.The deduced amino acid sequence predicts a molecular weight of approximately 28.83 kD and an isoelectric point of 9.21.Sequence analysis revealed no N-terminal signal peptide cleavage site,suggesting the absence of both a signal peptide and transmembrane regions in this protein.The amino acid sequence contains 2 N-terminal myristoylation sites,1 N-glycosylation site,1 glycosaminoglycan attachment site,4 microbody C-terminal targeting signal sites,3 casein kinase II phosphorylation sites,and 4 protein kinase C phosphorylation sites.Subcellular localization prediction showed that the CobQ protein is primarily localized in the cytoplasm(65.2%probability).Homology analysis demonstrated that the amino acid sequence of the cobQ gene from V.alginolyticus shares up to 99%homology with other Vibrio species,clustering within the same subclade as Vibrio parahaemolyticus,indicating close phylogenetic relationships.Secondary structure prediction revealed proportions ofα-helices,random coils,and extended strands as 44.40%,36.68%,and 18.92%,respectively.The tertiary structure model exhibited 87.62%similarity to the template A0A165XBE1.1.[Conclusions] In this study,the V.alginolyticus cobq gene was successfully cloned and its sequence was analyzed by bioinformatics.It is expected to lay a foundation for the subsequent study of the regulatory mechanism of its protein on the virulence of V.alginolyticus.展开更多
Objective:Tanshinone ⅡA,one of the most abundant liposoluble components isolated from the traditional Chinese medicine Salvia miltiorrhiza,exhibits significant biological activities in anti-inflammatory,antibacterial...Objective:Tanshinone ⅡA,one of the most abundant liposoluble components isolated from the traditional Chinese medicine Salvia miltiorrhiza,exhibits significant biological activities in anti-inflammatory,antibacterial,and antitumor eff ects.This study aims to systematically explore the mechanism of Tanshinone ⅡA through bioinformatics.Methods:We utilized the TCMSP database to retrieve the oral bioavailability(OB)and drug-likeness(DL)of Tanshinone ⅡA.The gene chip numbered GSE85871 was downloaded from the GEO database,and diff erential genes were analyzed using R language to identify potential targets of Tanshinone ⅡA.After obtaining these targets,GO analysis and KEGG pathway analysis were performed using the DAVID 6.8 database.Diseases related to Tanshinone ⅡA were explored through the CTD database.Finally,Cytoscape was employed to construct a visual network of multiple targets,pathways,and diseases associated with Tanshinone ⅡA.Results:Tanshinone ⅡA demonstrated good drug effi cacy with an OB value of 49.89%and a DL value of 0.4.A total of 132 potential targets were identifi ed,primarily exhibiting gene co-expression and physical interaction in the PPI network.These targets were enriched in biological processes and pathways such as ovarian steroidogenesis,cell cycle,and steroid hormone biosynthesis.Tanshinone ⅡA was found to be relevant in the treatment of diseases including breast tumors,hypertension,atherosclerosis,gliomas,vascular system injuries,left ventricular hypertrophy,leukemia,and hearing loss.Conclusion:Utilizing bioinformatics approaches,we systematically analyzed the possible molecular mechanisms of Tanshinone ⅡA,providing potential targets and insights into its pharmacological mechanisms and treatment strategies.展开更多
Objective To predict the autophagy-related pathogenesis and key diagnostic genes of diabetic kidney disease(DKD)through bioinformatics analysis,and to identify related Chinese medicines.Methods Data from sequencing mi...Objective To predict the autophagy-related pathogenesis and key diagnostic genes of diabetic kidney disease(DKD)through bioinformatics analysis,and to identify related Chinese medicines.Methods Data from sequencing microarrays GSE30528,GSE30529,and GSE1009 in the Gene Expression Omnibus(GEO)were employed.Differentially expressed genes(DEGs)with adjusted P<0.05 from GSE30528 and GSE30529 were identified.Combining these DEGs with the human autophagy gene database,Gene Ontology(GO),Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analyses,and protein-protein interaction(PPI)network analysis were conducted on the obtained DKD autophagy-related genes.Subsequently,the least absolute shrinkage and selection operator(LASSO)regression and support vector machinerecursive feature elimination(SVM-RFE)algorithms were adopted to select autophagy-related genes.The diagnostic capability of these genes was assessed through analysis with the external validation set from microarray GSE1009,and relevant Chinese medicines were inversely predicted using the SymMap database.Results A total of 2014 DEGs were selected from GSE30528 and GSE30529,leading to the identification of 37 DKD autophagy-related genes.GO analysis indicated 681 biological mechanisms,including autophagy regulation and plasma membrane microdomain activity.KEGG enrichment analysis identified 112 related signaling pathways.PPI network analysis showed a marked enrichment of autophagy-related genes in DKD.Through LASSO regression and SVM-RFE,four core diagnostic genes for autophagy in DKD were identified:protein phosphatase 1 regulatory subunit 15A(PPP1R15A),hypoxia inducible factor 1 alpha subunit(HIF1α),deleted in liver cancer 1(DLC1),and ceroid lipofuscinosis neuronal 3(CLN3).The external validation set demonstrated high diagnostic efficiency for these genes.Finally,146 kinds of potential Chinese medicines were predicted using the SymMap database,with heatclearing and detoxifying medicine and blood-activating and stasis-eliminating medicine accounting for the largest proportion(25/146 and 13/146,respectively).Conclusion This study analyzed and validated bioinformatics sequencing databases to elucidate the potential molecular mechanisms of DKD autophagy and predicted key diagnostic genes,potential therapeutic targets,and related Chinese medicines,laying a solid foundation for clinical research and application.展开更多
[Objectives]This study was conducted to investigate the functional characteristics of the trxB gene in Vibrio alginolyticus.[Methods]A pair of specific primers was designed based on the trxB gene sequence of V.alginol...[Objectives]This study was conducted to investigate the functional characteristics of the trxB gene in Vibrio alginolyticus.[Methods]A pair of specific primers was designed based on the trxB gene sequence of V.alginolyticus for PCR cloning of its full-length sequence.Systematic bioinformatics analyses were conducted to predict the physicochemical properties,secondary structure,and tertiary structure of the encoded protein.[Results]The trxB gene is 960 bp in length,encoding 319 amino acid residues.The deduced protein has a predicted molecular weight of 34.32 kDa and an isoelectric point(pI)of 4.77.Analysis of the amino acid sequence revealed a distinct signal peptide cleavage site at the N-terminus,with no transmembrane domains.The functional sites are as follows:1 N-glycosylation site,1 cAMP-and cGMP-dependent protein kinase phosphorylation site,4 protein kinase C phosphorylation sites,7 casein kinase II phosphorylation sites,1 tyrosine kinase phosphorylation site,11 N-myristoylation sites,1 prenyl group binding site,3 microbody C-terminal targeting signal sites,and 1 xanthine nucleotide-disulfide oxidoreductase class II active site.Subcellular localization prediction indicated the highest probability(44.4%)for endoplasmic reticulum localization.The TrxB amino acid sequence of V.alginolyticus shares 97.2%-98.4%homology with other Vibrio species,and they were clustered within the same subgroup.Secondary structure prediction showed proportions of random coils(31.97%),alpha-helices(31.66%),extended strands(25.08%),and beta turns(11.29%).The tertiary structure model exhibited 88.68%similarity to template 5vt3.1.A.[Conclusions]This study elucidated the characterization of the TrxB protein in V.alginolyticus,laying a theoretical foundation for the development of outer membrane protein subunit vaccines against this pathogen.展开更多
Background:In regard to head and neck squamous cell carcinoma(HNSC),a common type of head and neck malignant tumor with high mortality,the role of Piezo-type mechanosensitive ion channel component 1(PIEZO1)is poorly u...Background:In regard to head and neck squamous cell carcinoma(HNSC),a common type of head and neck malignant tumor with high mortality,the role of Piezo-type mechanosensitive ion channel component 1(PIEZO1)is poorly understood.PIEZO1,a mechanosensitive ion channel,is implicated in tumorigenesis,but its expression,prognostic significance,and mechanisms in HNSC remain unclear.Our study aimed to clarify these aspects through in vitro experiments and bioinformatics analyses.Methods:In order to investigate PIEZO1 expression in normal and cancerous tissues,we used The Cancer Genome Atlas data.Our bioinformatics analyses explored PIEZO1 mRNA expression,correlations,survival curves,upstream mRNA targets,and coexpressed genes.Gene Ontology analysis functionally annotated these coexpressed genes,and pathway enrichment studies further clarified their roles.In addition,we conducted in vitro experiments to examine and compare PIEZO1 expression in normal and cancerous human tissue samples.We performed immunohistochemical analyses to detect PIEZO1 expression in human HNSC tissues.Results:Our results have revealed significantly elevated PIEZO1 expression in HNSC tissue samples compared with adjacent noncancerous tissues.Bioinformatics analysis further showed that PIEZO1 expression was notably higher in high-grade HNSC tumors and was associated with lower survival rates.OncomiR database analysis showed that the downregulation of hsa-miR-101-3p correlated with increased PIEZO1 expression in HNSC.Mechanistic studies identified 4 focal adhesion-related genes(ITGA5,LAMC2,PXN,and VEGFC)modulated by PIEZO1.These findings underscore the potential of PIEZO1 as a therapeutic target and prognostic marker for HNSC.Conclusions:Our study has revealed the expression profile of PIEZO1 in HNSC,emphasizing its potential as a diagnostic and therapeutic target along with hsa-miR-101-3p.展开更多
Bacillus velezensis is a Gram-positive and spore-forming bacterium.It has potent antimicrobial properties that can be used to promote plant growth and as a pesticide by inhibiting pathogens.B.velezensis has the capabi...Bacillus velezensis is a Gram-positive and spore-forming bacterium.It has potent antimicrobial properties that can be used to promote plant growth and as a pesticide by inhibiting pathogens.B.velezensis has the capability to generate a diverse range of enzymes that have potential applications in various fields,such as enzyme production,fermented food,degradation of pollutants,and bioenergy.In addition,B.velezensis is a promising probiotic.It possesses high bile-salt tolerance characteristics and has a high success rate of colonization in the intestinal mucosa.Besides,the strain can also regulate gut microbiota constitute by increasing the number of beneficial microorganisms and decreasing the number of pathogens.Furthermore,based on its special properties,including high-yield protease production and high salt-tolerance,B.velezensis shows potential for use in marine protein fermentation,opening up new avenues for the development of novel food products and bioactive peptides.In addition,B.velezensis can shorten the fermentation time as well as improve the nutritional value and flavor of fermented food.The safety of B.velezensis for food production was evaluated.This review provides valuable insights into the potential uses and benefits of B.velezensis,particularly in the context of fermented foods.展开更多
Recent studies have found that erythropoietin promotes the recovery of neurological function after traumatic brain injury.However,the precise mechanism of action remains unclea r.In this study,we induced moderate trau...Recent studies have found that erythropoietin promotes the recovery of neurological function after traumatic brain injury.However,the precise mechanism of action remains unclea r.In this study,we induced moderate traumatic brain injury in mice by intrape ritoneal injection of erythro poietin for 3 consecutive days.RNA sequencing detected a total of 4065 differentially expressed RNAs,including 1059 mRNAs,92 microRNAs,799 long non-coding RNAs,and 2115circular RNAs.Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses revealed that the coding and non-coding RNAs that were differentially expressed after traumatic brain injury and treatment with erythropoietin play roles in the axon guidance pathway,Wnt pathway,and MAPK pathway.Constructing competing endogenous RNA networks showed that regulatory relationship between the differentially expressed non-coding RNAs and mRNAs.Because the axon guidance pathway was repeatedly enriched,the expression of Wnt5a and Ephb6,key factors in the axonal guidance pathway,was assessed.Ephb6 expression decreased and Wnt5a expression increased after traumatic brain injury,and these effects were reversed by treatment with erythro poietin.These findings suggest that erythro poietin can promote recove ry of nerve function after traumatic brain injury through the axon guidance pathway.展开更多
This study aimed to investigate the potential mechanisms underlying the therapeutic effects of Fructus Ligustri Lucidi in the treatment of diabetic nephropathy(DN)through bioinformatics analysis.The research commenced...This study aimed to investigate the potential mechanisms underlying the therapeutic effects of Fructus Ligustri Lucidi in the treatment of diabetic nephropathy(DN)through bioinformatics analysis.The research commenced with a comprehensive database search for DN-associated datasets and gene targets of Fructus Ligustri Lucidi.Subsequently,the ssGSEA method was employed to score the drug target gene sets,and based on these scores,subjects were categorized.Further analysis involved differential analysis and enrichment analysis techniques to elucidate differentially expressed genes(DEGs)and associated pathways between the two groups.Based on the ssGSEA scoring results,the data were stratified into two groups:the"High NZZ group"and the"Low NZZ group".Through differential analysis,a total of 18 DEGs were identified,comprising 14 upregulated genes(EGR1,CCL2,CDH6,VCAN-AS1,VCAN,C3,MMP7,RNASE6,C1QC,MOXD1,APOC1,SFRP2,CCL21,and LUM)and four downregulated genes(OTTHUMG00000152025,RERG,B3GALT2,and NELL1).Notably,several genes exhibited concurrent expression patterns in both the DN and High NZZ groups,including VCAN-AS1,CCL21,VCAN,MOXD1,CCL2,SFRP2,MMP7,C3,RNASE6,LUM,C1QC,APOC1,and CDH6.Enrichment analysis revealed significant enrichment in pathways related to"regulation of apoptotic cell clearance"and"granulocyte chemotaxis",among others.These findings highlighted the potential value of Fructus Ligustri Lucidi in the treatment of DN and unveiled novel potential targets for prognosis and therapy in DN patients.This study offered promising avenues for enhancing both the prognosis and treatment outcomes for individuals affected by this condition.展开更多
BACKGROUND Gastric cancer(GC)is one of the most aggressive malignancies with limited therapeutic options and a poor prognosis.Resveratrol,a non-flavonoid poly-phenolic compound found in a variety of Chinese medicinal ...BACKGROUND Gastric cancer(GC)is one of the most aggressive malignancies with limited therapeutic options and a poor prognosis.Resveratrol,a non-flavonoid poly-phenolic compound found in a variety of Chinese medicinal materials,has shown excellent anti-GC effect.However,its exact mechanisms of action in GC have not been clarified.AIM To identify the effects of resveratrol on GC progression and explore the related molecular mechanisms.METHODS Action targets of resveratrol and GC-related targets were screened from public databases.The overlapping targets between the two were confirmed using a Venn diagram,and a“Resveratrol-Target-GC”network was constructed using Cyto-scape software version 3.9.1.The protein-protein interaction(PPI)network was constructed using STRING database and core targets were identified by PPI network analysis.The Database for Annotation,Visualization and Integrated A total of 378 resveratrol action targets and 2154 GC disease targets were obtained from public databases,and 181 intersection targets between the two were screened by Venn diagram.The top 20 core targets were identified by PPI network analysis of the overlapping targets.GO function analysis mainly involved protein binding,identical protein binding,cytoplasm,nucleus,negative regulation of apoptotic process and response to xenobiotic stimulus.KEGG enrichment analysis suggested that the involved signaling pathways mainly included PI3K-AKT signaling pathway,MAPK signaling pathway,IL-17 signaling pathway,TNF signaling pathway,ErbB signaling pathway,etc.FBJ murine osteosarcoma viral oncogene homolog(FOS)and matrix metallopeptidase 9(MMP9)were selected by differential expression analysis,and they were closely associated with immune infiltration.Molecular docking results showed that resveratrol docked well with these two targets.Resveratrol treatment arrested the cell cycle at the S phase,induced apoptosis,and weakened viability,migration and invasion in a dose-dependent manner.Furthermore,resveratrol could exhibit anti-GC effect by regulating FOS and MMP9 expression.CONCLUSION The anti-GC effects of resveratrol are related to the inhibition of cell proliferation,migration,invasion and induction of cell cycle arrest and apoptosis by targeting FOS and MMP9.展开更多
BACKGROUND Circular RNAs(circRNAs)are involved in the pathogenesis of many diseases through competing endogenous RNA(ceRNA)regulatory mechanisms.AIM To investigate a circRNA-related ceRNA regulatory network and a new ...BACKGROUND Circular RNAs(circRNAs)are involved in the pathogenesis of many diseases through competing endogenous RNA(ceRNA)regulatory mechanisms.AIM To investigate a circRNA-related ceRNA regulatory network and a new predictive model by circRNA to understand the diagnostic mechanism of circRNAs in ulcerative colitis(UC).METHODS We obtained gene expression profiles of circRNAs,miRNAs,and mRNAs in UC from the Gene Expression Omnibus dataset.The circRNA-miRNA-mRNA network was constructed based on circRNA-miRNA and miRNA-mRNA interactions.Functional enrichment analysis was performed to identify the biological mechanisms involved in circRNAs.We identified the most relevant differential circRNAs for diagnosing UC and constructed a new predictive nomogram,whose efficacy was tested with the C-index,receiver operating characteristic curve(ROC),and decision curve analysis(DCA).RESULTS A circRNA-miRNA-mRNA regulatory network was obtained,containing 12 circRNAs,three miRNAs,and 38 mRNAs.Two optimal prognostic-related differentially expressed circRNAs,hsa_circ_0085323 and hsa_circ_0036906,were included to construct a predictive nomogram.The model showed good discrimination,with a C-index of 1(>0.9,high accuracy).ROC and DCA suggested that the nomogram had a beneficial diagnostic ability.CONCLUSION This novel predictive nomogram incorporating hsa_circ_0085323 and hsa_circ_0036906 can be conveniently used to predict the risk of UC.The circRNa-miRNA-mRNA network in UC could be more clinically significant.展开更多
基金Supported by School-Level Key Projects at Bengbu Medical College,No.2021byzd109.
文摘BACKGROUND Gallbladder neuroendocrine carcinoma(NEC)represents a subtype of gallbladder malignancies characterized by a low incidence,aggressive nature,and poor prognosis.Despite its clinical severity,the genetic alterations,mechanisms,and signaling pathways underlying gallbladder NEC remain unclear.CASE SUMMARY This case study presents a rare instance of primary gallbladder NEC in a 73-year-old female patient,who underwent a radical cholecystectomy with hepatic hilar lymphadenectomy and resection of liver segments IV-B and V.Targeted gene sequencing and bioinformatics analysis tools,including STRING,GeneMANIA,Metascape,TRRUST,Sangerbox,cBioPortal and GSCA,were used to analyze the biological functions and features of mutated genes in gallbladder NEC.Twelve mutations(APC,ARID2,IFNA6,KEAP1,RB1,SMAD4,TP53,BTK,GATA1,GNAS,and PRDM3)were identified,and the tumor mutation burden was determined to be 9.52 muts/Mb via targeted gene sequencing.A protein-protein interaction network showed significant interactions among the twelve mutated genes.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were used to assess mutation functions and pathways.The results revealed 40 tumor-related pathways.A key regulatory factor for gallbladder NEC-related genes was identified,and its biological functions and features were compared with those of gallbladder carcinoma.CONCLUSION Gallbladder NEC requires standardized treatment.Comparisons with other gallbladder carcinomas revealed clinical phenotypes,molecular alterations,functional characteristics,and enriched pathways.
文摘Bioinformatics,an interdisciplinary field that integrates computer science,biology,information technology,and statistics,plays a pivotal role in analyzing and interpreting biological data.It has become an indispensable tool in the design and discovery of novel drugs by facilitating the analysis of biological datasets and aiding in the identification of potential therapeutic targets.With the rise of antibiotic resistance among bacterial species,the demand for new drug development has intensified.However,the process of drug discovery remains labor-intensive,costly,and time-consuming.The identification of new drugs involves multiple critical stages,including target identification,structural analysis of the target protein,selection of potential drug candidates,safety and efficacy assessments,drug optimization,and ultimately,validation.Bioinformatics contributes significantly to each of these phases.For instance,through the analysis of protein sequences and genetic data,researchers can pinpoint potential drug targets.Once a target protein is identified,bioinformatics tools enable detailed structural analysis of the protein.Upon locating the potential ligand-binding site,large compound databases can be screened to discover viable drug candidates.Simulations further aid in examining the interaction between the target protein and biomolecules,providing valuable insights into the drug’s safety and efficacy.Moreover,bioinformatics-driven drug optimization helps improve both safety and effectiveness.Recent advances,such as pharmacophore modeling and molecular docking techniques,have accelerated the screening process,narrowing thousands of candidate molecules down to a select few with promising therapeutic potential.In this study,bioinformatics was leveraged within the framework of network pharmacology to design and discover new drugs.
基金Supported by Zhejiang Provincial Natural Science Foundation of China,No.LQ23H020004The Medical and Health Research Project of Zhejiang province,No.2024KY983Basic Medical Health Technology Project of Wenzhou Science and Technology Bureau,No.Y20210818 and No.Y20210140.
文摘BACKGROUND Myocardial ischemia/reperfusion(I/R)injury,which is associated with high morbidity and mortality,is a main cause of unexpected myocardial injury after acute myocardial infarction.However,the underlying mechanism remains unclear.Circular RNAs(circRNAs),which are formed from protein-coding genes,can sequester microRNAs or proteins,modulate transcription and interfere with splicing.Authoritative studies suggest that circRNAs may play an important role in myocardial I/R injury.AIM To explore the role and mechanism of circRNAs in myocardial I/R injury.METHODS We constructed a myocardial I/R injury model using ligation of the left anterior descending coronary artery,and evaluated the success of the validated model using triphenyltetrazolium chloride and hematoxylin-eosin staining.Then,left ventricular samples from different groups were selected for mRNA-sequence,and differential gene screening was performed on the obtained results.The differentially obtained mRNAs were divided into up-regulated and down-regulated according to their expression levels,and Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)functional enrichment analysis were performed,respectively.Then,the obtained circRNA and microRNA(miRNA)were paired for analysis,and the binding sites of miRNA and mRNA were virtual screened.Finally,the obtained circRNA,miRNA and mRNA were constructed by ceRNA mutual most useful network.RESULTS We used an RNA sequencing array to investigate the expression signatures of circRNAs in myocardial I/R injury using three samples from the I/R group and three samples from the sham group.A total of 142 upregulated and 121 downregulated circRNAs were found to be differentially expressed(fold change≥2,P<0.05).GO and KEGG functional analyses of these circRNAs were performed.GO analysis revealed that these circRNAs were involved mainly in cellular and intracellular processes.KEGG analysis demonstrated that 6 of the top 20 pathways were correlated with cell apoptosis.Furthermore,a circRNA-miRNA coexpression network and ceRNA network based on these genes were constructed,revealing that mmu-circ-0001452,mmu-circ-0001637,and mmu-circ-0000870 might be key regulators of myocardial I/R injury.CONCLUSION This research provides new insights into the mechanism of myocardial I/R,which mmu-circ-0001452,mmu-circ-0001637,and mmu-circ-0000870 are expected to be new therapeutic targets for myocardial I/R injury.
基金supported by the National Natural Science Foundation of China(32470676 and 32170236)Central Guidance on Local Science and Technology Development Fund of Hebei Province(246Z2508G)+2 种基金Hebei Natural Science Foundation(C2020209064)Tangshan Science and Technology Program Project(21130217C)Key research project of North China University of Science and Technology(ZD-YG-202313-23).
文摘As a high-value eudicot family,many famous horticultural crop genomes have been deciphered in Oleaceae.However,there are currently no bioinformatics platforms focused on empowering genome research in Oleaceae.Herein,we developed the first comprehensive Oleaceae Genome Research Platform(OGRP,https://oleaceae.cgrpoee.top/).In OGRP,70 genomes of 10 Oleaceae species and 46 eudicots and 366 transcriptomes involving 18 Oleaceae plant tissues can be obtained.We built 34 window-operated bioinformatics tools,collected 38 professional practical software programs,and proposed 3 new pipelines,namely ancient polyploidization identification,ancestral karyotype reconstruction,and gene family evolution.Employing these pipelines to reanalyze the Oleaceae genomes,we clarified the polyploidization,reconstructed the ancestral karyotypes,and explored the effects of paleogenome evolution on genes with specific biological regulatory roles.Significantly,we generated a series of comparative genomic resources focusing on the Oleaceae,comprising 108 genomic synteny dot plots,1952225 collinear gene pairs,multiple genome alignments,and imprints of paleochromosome rearrangements.Moreover,in Oleaceae genomes,researchers can efficiently search for 1785987 functional annotations,22584 orthogroups,29582 important trait genes from 74 gene families,12664 transcription factor-related genes,9178872 transposable elements,and all involved regulatory pathways.In addition,we provided downloads and usage instructions for the tools,a species encyclopedia,ecological resources,relevant literatures,and external database links.In short,ORGP integrates rich data resources and powerful analytical tools with the characteristic of continuous updating,which can efficiently empower genome research and agricultural breeding in Oleaceae and other plants.
基金Guangzhou University of Chinese Medicine Shenzhen Hospital(Futian)Postdoctoral Foundation。
文摘This study aimed to investigate the role of autophagy-related genes in osteoarthritis(OA)and evaluate the therapeutic potential of Eucommin A,a key lignan component derived from Eucommia ulmoides.Gene expression profiles from OA patients and healthy controls were retrieved from the Gene Expression Omnibus(GEO)database.Differentially expressed genes(DEGs)were identified and intersected with autophagy-related genes from the Human Autophagy Database to pinpoint OA-specific autophagy candidates.Functional enrichment analyses via GO and KEGG highlighted involvement in nutrient response,apoptosis,and PI3K-Akt/FoxO signaling pathways.Core genes were prioritized using machine learning algorithms combined with protein-protein interaction(PPI)network analysis,followed by diagnostic validation in an independent cohort.Molecular docking and 100-ns molecular dynamics simulations were conducted to assess the binding stability between Eucommin A and the core targets.Interaction mechanisms were characterized using root mean square deviation(RMSD),root mean square fluctuation(RMSF),radius of gyration(Rg),and MM/GBSA binding free energy calculations.Among 2436 DEGs,56 were autophagy-related and significantly enriched in key biological processes.Machine learning identified EGFR,MAPK3,and MAPK8 as hub genes,with EGFR and MAPK8 exhibiting significant diagnostic value(AUC>0.5).Eucommin A demonstrated strong binding affinity to EGFR and MAPK8 via hydrogen bonding and hydrophobic interactions.Molecular dynamics simulations confirmed stable ligand-target complexes and favorable binding free energy profiles.These findings suggested EGFR and MAPK8 as diagnostic biomarkers for OA-related autophagy.Moreover,Eucommin A exerted multi-target therapeutic effects by stabilizing these autophagy-related proteins,proposing a novel strategy for OA treatment through modulation of autophagy.
文摘Objective:Employing bioinformatics methodologies to identify core genes intricately associated with the pathogenesis and progression of gastric cancer,and to evaluate their clinical significance.Method:Gene expression datasets GSE19826 and GSE13911 were acquired from the Gene Expression Omnibus(GEO).Differential gene expression analysis was conducted using GEO2R.Common differentially expressed genes(DEGs)were discerned via Venn diagram analysis on a bioinformatics platform.Functional enrichment analyses,including Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG),were performed on these overlapping DEGs.A protein-protein interaction(PPI)network was constructed with the STRING database,and central hub genes were identified using Cytoscape software.The expression profiles,prognostic value,and immune infiltration correlations of these key genes were further examined utilizing the GEPIA,Kaplan-Meier plotter,Human Protein Atlas(HPA),and TIMER databases.Results:Analysis revealed 120 commonly differentially expressed genes.These genes were significantly enriched in biological pathways concerning muscle cell cytoskeleton regulation,nutrient absorption,and extracellular matrix receptor interactions.PPI network analysis highlighted 10 core genes,including COL1A1,COL1A2,BGN,THBS2,COL5A2,and TIMP1.These genes exhibited marked upregulation in GC tissues.Statistical evaluation confirmed a significant link between their elevated expression and unfavorable patient outcomes(P<0.01).Furthermore,immune infiltration assessment indicated a positive correlation between the expression of these genes and macrophage infiltration within the tumor microenvironment,implying their involvement in modulating the immune response in GC,which could affect tumor behavior and clinical progression.Conclusion:The six genes identified may function as diagnostic biomarkers and represent promising therapeutic targets for gastric cancer.
基金the National Natural Science Foundation of China(82222075).
文摘Objective:To investigate the potential targets and mechanisms of Draconis Sanguis(DS),a valuable traditional Chinese medicine derived from the resin of the palm tree Daemonorops draco Bl(D.Sanguis,Xue Jie),in the treatment of myocardial infarction(MI).Methods:We explored the potential mechanisms of DS in the treatment of MI using network pharmacology,bioinformatic techniques,and transcriptomic analysis,followed by validation through in vivo and in vitro experiments.Results:Network pharmacology and bioinformatic analyses identified five genes(Fpr1,Glul,Mme,Mmp9,and Pla2g7)as potential targets for MI treatment.Moreover,DS significantly ameliorated cardiac function,inflammatory responses,and MI-induced myocardial fibrosis in vivo.Transcriptomic and bioinformatic analyses identified Pla2g7 as the most critical target in the DS treatment of MI.Molecular docking revealed that the key active ingredient in DS has a strong affinity for this gene.Furthermore,DS reduced the expression of Pla2g7(P=.0009),NLRP3(P=.003),interleukin-18(P<.001),and interleukin-1b(P=.004)mRNAs in vivo.Conclusions:The results indicate that DS can downregulate the expression of Pla2g7 and reduce the inflammatory response.This demonstrates the potential therapeutic target of DS and the mechanism underlying its cardioprotective effects.
基金Supported by the National Key R&D Program of China,No.2022YFC2503700 and No.2022YFC2503703the National Health Commission Key Laboratory of Nuclear Technology Medical Transformation(Mianyang Central Hospital),No.2023HYX005.
文摘BACKGROUND Esophageal cancer(ESCA)poses a significant challenge in oncology because of the limited treatment options and poor prognosis.Therefore,enhancing the therapeutic effects of radiotherapy for ESCA and identifying relevant therapeutic targets are crucial for improving both the survival rate and quality of life of patients.AIM To define the role of the transcription factor Snail family transcriptional repressor 1(SNAI1)in ESCA,particularly its regulation of radiosensitivity.METHODS A comprehensive analysis of TCGA data assessed SNAI1 expression in ESCA.Survival curves correlated SNAI1 levels with radiotherapy outcomes.Colony formation assays,flow cytometry,and a xenograft model were used to evaluate tumor radiosensitivity and apoptosis.Western blot validated protein expression,while Chromatin im-munoprecipitation assays examined SNAI1's role in regulating epithelial-mesenchymal transition(EMT).RESULTS SNAI1 expression in ESCA cell lines and clinical specimens emphasizes its central role in this disease.Elevated SNAI1 expression is correlated with unfavorable outcomes in radiotherapy.Downregulation of SNAI1 enhances the sensitivity of ESCA cells to ionizing radiation(IR),resulting in remarkable tumor regression upon IR treatment in vivo.This study underscores the direct involvement of SNAI1 in the regulation of EMT,particularly under IR-induced conditions.Furthermore,inhibiting deacetylation effectively suppresses EMT,suggesting a potential avenue to enhance the response to radiotherapy in ESCA.CONCLUSION This study highlights SNAI1's role in ESCA radiosensitivity,offering prognostic insights and therapeutic strategies to enhance radiotherapy by targeting SNAI1 and modulating EMT processes.
基金Supported by Natural Science Foundation of Guangdong Province(2025A1515011061)Outstanding Graduate Entering Laboratory Project of College of Fisheries,Guangdong Ocean University+1 种基金Undergraduate Innovation and Entrepreneurship Training Program of Guangdong Ocean University(CXXL2024007)Undergraduate Innovation Team of Guangdong Ocean University(CCTD201802).
文摘[Objectives]To develop a pair of specific primers for the PCR amplification of the full-length relA gene from Vibrio alginolyticus strain HY9901,as well as to conduct bioinformatics analysis.[Methods]The relA gene was amplified through PCR,and the resulting gene sequence was subsequently analyzed using bioinformatics tools,including amino acid sequence prediction,functional site analysis,subcellular localization prediction,and homology comparison.[Results]The relA gene had a total length of 2220 bp and encoded 739 amino acid residues.The molecular weight was approximately 84.1261 kDa,and its isoelectric point was 5.95.The protein lacked a signal peptide and transmembrane regions,while exhibiting multiple phosphorylation sites.Predictions regarding its subcellular localization suggested that it was predominantly situated in the cytoplasm.The amino acid sequence demonstrated a homology of 97%to 99%with other species within the genus Vibrio,and it clustered within the same subfamily as V.antiquarius and V.diabolicus.In the prediction of secondary structure,the proportions ofα-helix,extended strand,random coil,andβ-sheet were 54.13%,12.04%,28.15%and 5.68%,respectively.The similarity between the tertiary structure model and template 5kpw.1.w was 66%.[Conclusions]In this study,the relA gene of V.alginolyticus strain HY9901 has been successfully amplified and analyzed.The structural characteristics and potential functions of the encoded protein have been elucidated,thereby providing foundational data for understanding the role of this gene in V.alginolyticus.
基金Supported by College Student Innovation and Entrepreneurship Training Program(S202210553003)Hunan Provincial Education Department Outstanding Youth Research Project(23B0820).
文摘Kinesins are a superfamily of proteins widely present in eukaryotes,playing crucial roles in plant cell wall assembly,cell elongation regulation,gravity sensing,and fertility control.In this study,bioinformatics analysis of the OsKMP2 gene(LOC_Os02g28850)was performed using online tools such as ExPASy-ProtParam,ProtScale,CD-search,and DNAMAN software.Additionally,qRT-PCR was employed to analyze the tissue expression pattern of OsKMP2.The results showed that the molecular weight of the OsKMP2 is 118.39728 kDa,and it is a hydrophilic and unstable acidic protein.Secondary structure prediction revealed that it primarily consists ofα-helices(69.45%),random coils(25.19%),and extended strands(5.36%).The gene was expressed in various rice tissues,with the highest expression level observed in leaves.These results indicate that the OsKMP2 gene exhibits high evolutionary conservation and functional diversity in rice.
基金Natural Science Foundation of Guangdong Province(2025A1515011061)Outstanding Graduate Entering Laboratory Project of College of Fisheries,Guangdong Ocean University+1 种基金Undergraduate Innovation and Entrepreneurship Training Program of Guangdong Ocean University(CXXL2024007)Undergraduate Innovation Team of Guangdong Ocean University(CCTD201802).
文摘[Objectives] To analyze the function of cobQ gene from Vibrio alginolyticus strain HY9901,and to provide a reference for exploring the possible mechanism of cobQ gene from V.alginolyticus.[Methods] A pair of primers were designed based on the sequence of the V.alginolyticus cobQ gene and used to amplify the full-length gene by PCR.[Results] The PCR amplification results indicated that the cobQ gene has a full length of 780 bp,encoding 259 amino acid residues.The deduced amino acid sequence predicts a molecular weight of approximately 28.83 kD and an isoelectric point of 9.21.Sequence analysis revealed no N-terminal signal peptide cleavage site,suggesting the absence of both a signal peptide and transmembrane regions in this protein.The amino acid sequence contains 2 N-terminal myristoylation sites,1 N-glycosylation site,1 glycosaminoglycan attachment site,4 microbody C-terminal targeting signal sites,3 casein kinase II phosphorylation sites,and 4 protein kinase C phosphorylation sites.Subcellular localization prediction showed that the CobQ protein is primarily localized in the cytoplasm(65.2%probability).Homology analysis demonstrated that the amino acid sequence of the cobQ gene from V.alginolyticus shares up to 99%homology with other Vibrio species,clustering within the same subclade as Vibrio parahaemolyticus,indicating close phylogenetic relationships.Secondary structure prediction revealed proportions ofα-helices,random coils,and extended strands as 44.40%,36.68%,and 18.92%,respectively.The tertiary structure model exhibited 87.62%similarity to the template A0A165XBE1.1.[Conclusions] In this study,the V.alginolyticus cobq gene was successfully cloned and its sequence was analyzed by bioinformatics.It is expected to lay a foundation for the subsequent study of the regulatory mechanism of its protein on the virulence of V.alginolyticus.
文摘Objective:Tanshinone ⅡA,one of the most abundant liposoluble components isolated from the traditional Chinese medicine Salvia miltiorrhiza,exhibits significant biological activities in anti-inflammatory,antibacterial,and antitumor eff ects.This study aims to systematically explore the mechanism of Tanshinone ⅡA through bioinformatics.Methods:We utilized the TCMSP database to retrieve the oral bioavailability(OB)and drug-likeness(DL)of Tanshinone ⅡA.The gene chip numbered GSE85871 was downloaded from the GEO database,and diff erential genes were analyzed using R language to identify potential targets of Tanshinone ⅡA.After obtaining these targets,GO analysis and KEGG pathway analysis were performed using the DAVID 6.8 database.Diseases related to Tanshinone ⅡA were explored through the CTD database.Finally,Cytoscape was employed to construct a visual network of multiple targets,pathways,and diseases associated with Tanshinone ⅡA.Results:Tanshinone ⅡA demonstrated good drug effi cacy with an OB value of 49.89%and a DL value of 0.4.A total of 132 potential targets were identifi ed,primarily exhibiting gene co-expression and physical interaction in the PPI network.These targets were enriched in biological processes and pathways such as ovarian steroidogenesis,cell cycle,and steroid hormone biosynthesis.Tanshinone ⅡA was found to be relevant in the treatment of diseases including breast tumors,hypertension,atherosclerosis,gliomas,vascular system injuries,left ventricular hypertrophy,leukemia,and hearing loss.Conclusion:Utilizing bioinformatics approaches,we systematically analyzed the possible molecular mechanisms of Tanshinone ⅡA,providing potential targets and insights into its pharmacological mechanisms and treatment strategies.
基金National Natural Science Foundation of China(82170747),and Shanghai Key Laboratory of Traditional Chinese Clinical Medicine(20DZ2272200).
文摘Objective To predict the autophagy-related pathogenesis and key diagnostic genes of diabetic kidney disease(DKD)through bioinformatics analysis,and to identify related Chinese medicines.Methods Data from sequencing microarrays GSE30528,GSE30529,and GSE1009 in the Gene Expression Omnibus(GEO)were employed.Differentially expressed genes(DEGs)with adjusted P<0.05 from GSE30528 and GSE30529 were identified.Combining these DEGs with the human autophagy gene database,Gene Ontology(GO),Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analyses,and protein-protein interaction(PPI)network analysis were conducted on the obtained DKD autophagy-related genes.Subsequently,the least absolute shrinkage and selection operator(LASSO)regression and support vector machinerecursive feature elimination(SVM-RFE)algorithms were adopted to select autophagy-related genes.The diagnostic capability of these genes was assessed through analysis with the external validation set from microarray GSE1009,and relevant Chinese medicines were inversely predicted using the SymMap database.Results A total of 2014 DEGs were selected from GSE30528 and GSE30529,leading to the identification of 37 DKD autophagy-related genes.GO analysis indicated 681 biological mechanisms,including autophagy regulation and plasma membrane microdomain activity.KEGG enrichment analysis identified 112 related signaling pathways.PPI network analysis showed a marked enrichment of autophagy-related genes in DKD.Through LASSO regression and SVM-RFE,four core diagnostic genes for autophagy in DKD were identified:protein phosphatase 1 regulatory subunit 15A(PPP1R15A),hypoxia inducible factor 1 alpha subunit(HIF1α),deleted in liver cancer 1(DLC1),and ceroid lipofuscinosis neuronal 3(CLN3).The external validation set demonstrated high diagnostic efficiency for these genes.Finally,146 kinds of potential Chinese medicines were predicted using the SymMap database,with heatclearing and detoxifying medicine and blood-activating and stasis-eliminating medicine accounting for the largest proportion(25/146 and 13/146,respectively).Conclusion This study analyzed and validated bioinformatics sequencing databases to elucidate the potential molecular mechanisms of DKD autophagy and predicted key diagnostic genes,potential therapeutic targets,and related Chinese medicines,laying a solid foundation for clinical research and application.
基金Supported by Natural Science Foundation of Guangdong Province(2025A1515011061)Outstanding Graduate Entering Laboratory Project of College of Fisheries,Guangdong Ocean University+1 种基金Undergraduate Innovation and Entrepreneurship Training Program of Guangdong Ocean University(CXXL2024007)Undergraduate Innovation Team of Guangdong Ocean University(CCTD201802).
文摘[Objectives]This study was conducted to investigate the functional characteristics of the trxB gene in Vibrio alginolyticus.[Methods]A pair of specific primers was designed based on the trxB gene sequence of V.alginolyticus for PCR cloning of its full-length sequence.Systematic bioinformatics analyses were conducted to predict the physicochemical properties,secondary structure,and tertiary structure of the encoded protein.[Results]The trxB gene is 960 bp in length,encoding 319 amino acid residues.The deduced protein has a predicted molecular weight of 34.32 kDa and an isoelectric point(pI)of 4.77.Analysis of the amino acid sequence revealed a distinct signal peptide cleavage site at the N-terminus,with no transmembrane domains.The functional sites are as follows:1 N-glycosylation site,1 cAMP-and cGMP-dependent protein kinase phosphorylation site,4 protein kinase C phosphorylation sites,7 casein kinase II phosphorylation sites,1 tyrosine kinase phosphorylation site,11 N-myristoylation sites,1 prenyl group binding site,3 microbody C-terminal targeting signal sites,and 1 xanthine nucleotide-disulfide oxidoreductase class II active site.Subcellular localization prediction indicated the highest probability(44.4%)for endoplasmic reticulum localization.The TrxB amino acid sequence of V.alginolyticus shares 97.2%-98.4%homology with other Vibrio species,and they were clustered within the same subgroup.Secondary structure prediction showed proportions of random coils(31.97%),alpha-helices(31.66%),extended strands(25.08%),and beta turns(11.29%).The tertiary structure model exhibited 88.68%similarity to template 5vt3.1.A.[Conclusions]This study elucidated the characterization of the TrxB protein in V.alginolyticus,laying a theoretical foundation for the development of outer membrane protein subunit vaccines against this pathogen.
基金supported by grants from Hefei Municipal Health Commission,Hefei Municipal Finance Bureau(No.[2023]72).
文摘Background:In regard to head and neck squamous cell carcinoma(HNSC),a common type of head and neck malignant tumor with high mortality,the role of Piezo-type mechanosensitive ion channel component 1(PIEZO1)is poorly understood.PIEZO1,a mechanosensitive ion channel,is implicated in tumorigenesis,but its expression,prognostic significance,and mechanisms in HNSC remain unclear.Our study aimed to clarify these aspects through in vitro experiments and bioinformatics analyses.Methods:In order to investigate PIEZO1 expression in normal and cancerous tissues,we used The Cancer Genome Atlas data.Our bioinformatics analyses explored PIEZO1 mRNA expression,correlations,survival curves,upstream mRNA targets,and coexpressed genes.Gene Ontology analysis functionally annotated these coexpressed genes,and pathway enrichment studies further clarified their roles.In addition,we conducted in vitro experiments to examine and compare PIEZO1 expression in normal and cancerous human tissue samples.We performed immunohistochemical analyses to detect PIEZO1 expression in human HNSC tissues.Results:Our results have revealed significantly elevated PIEZO1 expression in HNSC tissue samples compared with adjacent noncancerous tissues.Bioinformatics analysis further showed that PIEZO1 expression was notably higher in high-grade HNSC tumors and was associated with lower survival rates.OncomiR database analysis showed that the downregulation of hsa-miR-101-3p correlated with increased PIEZO1 expression in HNSC.Mechanistic studies identified 4 focal adhesion-related genes(ITGA5,LAMC2,PXN,and VEGFC)modulated by PIEZO1.These findings underscore the potential of PIEZO1 as a therapeutic target and prognostic marker for HNSC.Conclusions:Our study has revealed the expression profile of PIEZO1 in HNSC,emphasizing its potential as a diagnostic and therapeutic target along with hsa-miR-101-3p.
基金financially supported by the Public Welfare Project of Zhoushan City,Zhejiang(2022C31050)。
文摘Bacillus velezensis is a Gram-positive and spore-forming bacterium.It has potent antimicrobial properties that can be used to promote plant growth and as a pesticide by inhibiting pathogens.B.velezensis has the capability to generate a diverse range of enzymes that have potential applications in various fields,such as enzyme production,fermented food,degradation of pollutants,and bioenergy.In addition,B.velezensis is a promising probiotic.It possesses high bile-salt tolerance characteristics and has a high success rate of colonization in the intestinal mucosa.Besides,the strain can also regulate gut microbiota constitute by increasing the number of beneficial microorganisms and decreasing the number of pathogens.Furthermore,based on its special properties,including high-yield protease production and high salt-tolerance,B.velezensis shows potential for use in marine protein fermentation,opening up new avenues for the development of novel food products and bioactive peptides.In addition,B.velezensis can shorten the fermentation time as well as improve the nutritional value and flavor of fermented food.The safety of B.velezensis for food production was evaluated.This review provides valuable insights into the potential uses and benefits of B.velezensis,particularly in the context of fermented foods.
基金supported by the National Natural Science Foundation of China,No.81771355the Natural Science Foundation of Chongqing Science and Technology Bureau,Nos.CSTC2015jcyjA10096,cstc2021jcyj-msxmX0262(all to ZL)。
文摘Recent studies have found that erythropoietin promotes the recovery of neurological function after traumatic brain injury.However,the precise mechanism of action remains unclea r.In this study,we induced moderate traumatic brain injury in mice by intrape ritoneal injection of erythro poietin for 3 consecutive days.RNA sequencing detected a total of 4065 differentially expressed RNAs,including 1059 mRNAs,92 microRNAs,799 long non-coding RNAs,and 2115circular RNAs.Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses revealed that the coding and non-coding RNAs that were differentially expressed after traumatic brain injury and treatment with erythropoietin play roles in the axon guidance pathway,Wnt pathway,and MAPK pathway.Constructing competing endogenous RNA networks showed that regulatory relationship between the differentially expressed non-coding RNAs and mRNAs.Because the axon guidance pathway was repeatedly enriched,the expression of Wnt5a and Ephb6,key factors in the axonal guidance pathway,was assessed.Ephb6 expression decreased and Wnt5a expression increased after traumatic brain injury,and these effects were reversed by treatment with erythro poietin.These findings suggest that erythro poietin can promote recove ry of nerve function after traumatic brain injury through the axon guidance pathway.
基金The National Natural Science Foundation of China(Grant No.81973486,82173974)State Administration of Tra ditional Chinese Medicine Processing Technology Inheritance Project(Grant No.202259)+2 种基金National Key Research and Development Pla n(Grant No.2018YFC1707002)Shanxi Provincial Basic Research Program General Project(Grant No.202203021211220)Study on Processing Synergistic Mechanism of Ligustrum aga inst Diabetic Nephropathy Based on TGFB1/Smads Pathway(Grant No.2024ZYYA021)。
文摘This study aimed to investigate the potential mechanisms underlying the therapeutic effects of Fructus Ligustri Lucidi in the treatment of diabetic nephropathy(DN)through bioinformatics analysis.The research commenced with a comprehensive database search for DN-associated datasets and gene targets of Fructus Ligustri Lucidi.Subsequently,the ssGSEA method was employed to score the drug target gene sets,and based on these scores,subjects were categorized.Further analysis involved differential analysis and enrichment analysis techniques to elucidate differentially expressed genes(DEGs)and associated pathways between the two groups.Based on the ssGSEA scoring results,the data were stratified into two groups:the"High NZZ group"and the"Low NZZ group".Through differential analysis,a total of 18 DEGs were identified,comprising 14 upregulated genes(EGR1,CCL2,CDH6,VCAN-AS1,VCAN,C3,MMP7,RNASE6,C1QC,MOXD1,APOC1,SFRP2,CCL21,and LUM)and four downregulated genes(OTTHUMG00000152025,RERG,B3GALT2,and NELL1).Notably,several genes exhibited concurrent expression patterns in both the DN and High NZZ groups,including VCAN-AS1,CCL21,VCAN,MOXD1,CCL2,SFRP2,MMP7,C3,RNASE6,LUM,C1QC,APOC1,and CDH6.Enrichment analysis revealed significant enrichment in pathways related to"regulation of apoptotic cell clearance"and"granulocyte chemotaxis",among others.These findings highlighted the potential value of Fructus Ligustri Lucidi in the treatment of DN and unveiled novel potential targets for prognosis and therapy in DN patients.This study offered promising avenues for enhancing both the prognosis and treatment outcomes for individuals affected by this condition.
基金Natural Science Foundation of Hebei Province,No.H2018307071Traditional Chinese Medicine Research Plan Project in Hebei Province,No.2022122Hebei Provincial Science and Technology Program,No.17397763D.
文摘BACKGROUND Gastric cancer(GC)is one of the most aggressive malignancies with limited therapeutic options and a poor prognosis.Resveratrol,a non-flavonoid poly-phenolic compound found in a variety of Chinese medicinal materials,has shown excellent anti-GC effect.However,its exact mechanisms of action in GC have not been clarified.AIM To identify the effects of resveratrol on GC progression and explore the related molecular mechanisms.METHODS Action targets of resveratrol and GC-related targets were screened from public databases.The overlapping targets between the two were confirmed using a Venn diagram,and a“Resveratrol-Target-GC”network was constructed using Cyto-scape software version 3.9.1.The protein-protein interaction(PPI)network was constructed using STRING database and core targets were identified by PPI network analysis.The Database for Annotation,Visualization and Integrated A total of 378 resveratrol action targets and 2154 GC disease targets were obtained from public databases,and 181 intersection targets between the two were screened by Venn diagram.The top 20 core targets were identified by PPI network analysis of the overlapping targets.GO function analysis mainly involved protein binding,identical protein binding,cytoplasm,nucleus,negative regulation of apoptotic process and response to xenobiotic stimulus.KEGG enrichment analysis suggested that the involved signaling pathways mainly included PI3K-AKT signaling pathway,MAPK signaling pathway,IL-17 signaling pathway,TNF signaling pathway,ErbB signaling pathway,etc.FBJ murine osteosarcoma viral oncogene homolog(FOS)and matrix metallopeptidase 9(MMP9)were selected by differential expression analysis,and they were closely associated with immune infiltration.Molecular docking results showed that resveratrol docked well with these two targets.Resveratrol treatment arrested the cell cycle at the S phase,induced apoptosis,and weakened viability,migration and invasion in a dose-dependent manner.Furthermore,resveratrol could exhibit anti-GC effect by regulating FOS and MMP9 expression.CONCLUSION The anti-GC effects of resveratrol are related to the inhibition of cell proliferation,migration,invasion and induction of cell cycle arrest and apoptosis by targeting FOS and MMP9.
基金Supported by the National Natural Science Foundation of China,No.81774093,No.81904009,No.81974546 and No.82174182Key R&D Project of Hubei Province,No.2020BCB001.
文摘BACKGROUND Circular RNAs(circRNAs)are involved in the pathogenesis of many diseases through competing endogenous RNA(ceRNA)regulatory mechanisms.AIM To investigate a circRNA-related ceRNA regulatory network and a new predictive model by circRNA to understand the diagnostic mechanism of circRNAs in ulcerative colitis(UC).METHODS We obtained gene expression profiles of circRNAs,miRNAs,and mRNAs in UC from the Gene Expression Omnibus dataset.The circRNA-miRNA-mRNA network was constructed based on circRNA-miRNA and miRNA-mRNA interactions.Functional enrichment analysis was performed to identify the biological mechanisms involved in circRNAs.We identified the most relevant differential circRNAs for diagnosing UC and constructed a new predictive nomogram,whose efficacy was tested with the C-index,receiver operating characteristic curve(ROC),and decision curve analysis(DCA).RESULTS A circRNA-miRNA-mRNA regulatory network was obtained,containing 12 circRNAs,three miRNAs,and 38 mRNAs.Two optimal prognostic-related differentially expressed circRNAs,hsa_circ_0085323 and hsa_circ_0036906,were included to construct a predictive nomogram.The model showed good discrimination,with a C-index of 1(>0.9,high accuracy).ROC and DCA suggested that the nomogram had a beneficial diagnostic ability.CONCLUSION This novel predictive nomogram incorporating hsa_circ_0085323 and hsa_circ_0036906 can be conveniently used to predict the risk of UC.The circRNa-miRNA-mRNA network in UC could be more clinically significant.
